Goals from Nwankwo Kanu, John Utaka and a late penalty by Matt Taylor left Nicolas Anelka's 13th minute opener a long and distant memory.
Bolton are already looking a side ripe for relegation even at this early stage of the season, after conceding eight goals in their opening three Premier League games
Heaven help them when they begin their UEFA Cup adventure, as that now appears to be an unwanted distraction rather than the celebratory reward of years gone by.
Portsmouth however are very much a team on the up and with Kanu back in vogue, Harry Redknapp's side are the ones who have shown they could be Bolton's replacement as perennial European football achievers.
In horrendous conditions on the South Coast it was Bolton who snatched the early initiative when El Hadji Diouf played Anelka through for the Frenchman to embarrass David James in the Pompey goal.
The former Arsenal striker used his electric pace to find the space between Djimi Traore and Hermann Hreidarsson before taking an early shot which skidded through James' legs.
Pompey needn't have worried though as three minutes later they hauled themselves back into the game with a goal straight out of Africa.
Gary O'Neil's clipped cross was touched down with the deftest of passes by Utaka for Kanu to stab his finish past Jussi Jaaskelainen.
The home side pressed on and Benjani Mwaruwari was then guilty of a glaring miss when another dangerous O'Neil cross left the Zimbabwean unmarked at the far post, but his header drifted over.
It was Utaka though who ultimately killed the game off as early as the 30th minute when he left the crowd gasping and Bolton's defence floundering, by bursting through to run half the length of the field and despatch a clever finish around Jaaskelainen.
Lee threw on Swedish international Christian Wilhelmsson at half-time in a bid to add more width to his side.
The former AS Roma midfielder had moments where he indicated he could be the answer to Bolton's problems.
Gary Speed saw a second-half header well saved by James from Wilhelmsson's cross which would have given Bolton an arguably undeserved equaliser.
Pompey though put the game beyond reasonable doubt two minutes from time. Substitute David Nugent played in Kanu for the Nigerian to be hacked down and Taylor step up to slot home the spot-kick.